Genomic in situ hybridization, a modification of fluorescence in situ hybridization technology, is one of the most exciting and versatile research tools to be developed in recent years. It has enabled plant chromosome and genome research to progress at phenomenal rate and its potential is far from exhausted. Genomic in situ hybridization has applications in characterization of genomes and chromosomes in hybrid polyploids, hybrid plants, partial allopolyploids, polyhaploids and recombinant breeding lines; and in the localization, and detection of amount of introgressed alien chromatin. Genomic in situ hybridization has also given new insights into somaclonal variation, the origin of B chromosomes, control of chromosome pairing and other aspects of chromosome evolution. This review highlights some of these areas and provides source material for the reader who seeks more information on a specific field.